To classify humanity is not that hard

By Razib Khan | December 14, 2010 12:22 pm

snpskinIn my post below I quoted my interview L. L. Cavalli-Sforza because I think it gets to the heart of some confusions which have emerged since the finding that most variation on any given locus is found within populations, rather than between them. The standard figure is that 85% of genetic variance is within continental races, and 15% is between them. You can see some Fst values on Wikipedia to get an intuition. Concretely, at a given locus X in population 1 the frequency of allele A may be 40%, while in population 2 it may be 45%. Obviously the populations differ, but the small difference is not going to be very informative of population substructure when most of the difference is within populations.

But there are loci which are much more informative. Interestingly, one controls variation on a trait which you are familiar with, skin color (unless you happen to lack vision). A large fraction (on the order of 25-40%) of the between population variance in the complexion of Africans and Europeans can be predicted by substitution on one SNP in the gene SLC24A5. The substitution has a major phenotypic effect, and, exhibits a great deal of between population variation. One variant is nearly fixed in Europeans, and another is nearly fixed in Africans. In other words the component of genetic variance on this trait that is between population is nearly 100%, not 15%. This illustrates that the 15% value was an average across the genome, and in fact there are significant differences on the genetic level which can be ancestrally informative. You can take this to the next level: increase the number of ancestrally informative markers to obtain a fine-grained picture of population structure. In the illustration above the top panel shows the frequencies at the SNP mentioned earlier on SLC24A5. The second panel shows variation at another SNP controlling skin color, SLC45A2. This second SNP is useful in separating South and Central Asians from Europeans and Middle Easterners, if not perfectly so. In other words, the more markers you have, the better your resolution of inter-population difference. This is why I found the following comment very interesting:

Razib’s final concession (that genetic variation exists) is revealing because I think that’s as far as the argument can really be taken. It’s a bit of a strawman, in that people who argue that race is entirely a social construct don’t actually deny that human genetic variation exists. What they deny is that there are non-arbitrary and mutually exclusive categories into which humans can be resolved. This is, I think, the point being made by the “Race by Fingerprints” etc. rhetorical device cited earlier.

In other words, it may be possible for any particular phenotypic trait or genetic locus to be resolved into a strictly cladistic system but humans, being an amalgam of such traits and locii, defy such resoution. So while the study of human genetic variation does, indeed, have “instrumental utility” the concept of biological races is, itself, an arcahic relic.

As I noted below, the comment doesn’t make sense. Here is a PCA of world populations using 250,000 markers:

lotsofmarkers

The relationships between individuals is hypothesis-free. That is, the two largest components of variance in the data just happen to produce clusters which neatly map onto geographic realities. If you think about this a little weird, it makes total sense: populations share a history of intermarriage, so over time they will develop population-specific distinctiveness. It may be true that most of the variance is between populations, but it is not difficult at all to discriminate populations, or generate clusters which are not arbitrary as a function of geography or social identity.

There are relationships which do not match intuition. Or at least intuition as it crystallized during the period of the rise of modern taxonomic science. The various phenotypically “black” peoples of the world, Africans, Melanesians, and some South Asians, do not cluster together. Rather, all non-Africans are separated from Africans by the largest component of variance within the data set. The traits used to make inferences of taxonomy in “folk biology” and early scientific attempts to generate a systematic tree of life in relation to the human races were not necessarily representative of total genome variation, which captures the evolutionary history of a population with greater accuracy and precision.

And obviously you don’t need 250,000 markers, let alone all ~3 billion base pairs in the human genome, to distinguish on the level of continental races/populations. A paper in 2002 laid out the parameters. δ is a measure of between population difference on genes.

sig1
sig2

From the paper:

…we can estimate that about 120 unselected SNPs or 20 highly selected SNPs can distinguish group CA from NA, AA from AS and AA from NA. A few hundred random SNPs are required to separate CA from AA, CA from AS and AS from NA, or about 40 highly selected loci. STRP loci are more powerful and have higher effective δ values because they have multiple alleles. Table 3 reveals that fewer than 100 random STRPs, or about 30 highly selected loci, can distinguish the major racial groups. As expected, differentiating Caucasians and Hispanic Americans, who are admixed but mostly of Caucasian ancestry, is more difficult and requires a few hundred random STRPs or about 50 highly selected loci. These results also indicate that many hundreds of markers or more would be required to accurately differentiate more closely related groups, for example populations within the same racial category.

The paper was written in 2002. Since then much has changed. Here is an image from a post from last summer:

village1

People within European villages tend to be relatively closely related. Again, it is totally reasonable that given enough markers you could assign individuals to different villages with a high confidence. Concretely, person X may show up in the pedigree of individuals from village 1 ~100 times at a given generation, while the same person may show up in the pedigree of individuals from village 2 ~10 times at a given generation. This isn’t rocket science, the basic logic as to why populations shake out based on geography and endogamy patterns is pretty obvious when you think about it.

At about the same time as the above work, A. W. F. Edwards, a statistical geneticist, published a paper titled Lewontin’s Fallacy which took direct aim at the misunderstand of the human Fst statistic and its relevance for classification. Here is Edwards answering why he wrote the article in 2002 (my co-blogger at GNXP, David B, is doing the questioning):

4. Your recent article on ‘Lewontin’s Fallacy’ criticises the claim that human geographical races have no biological meaning. As the article itself points out, it could have been written at any time in the last 30 years. So why did it take so long – and have you had any reactions from Lewontin or his supporters? [David B’s question -R]

I can only speak for myself as to why it took me so long. Others closer to the field will have to explain why the penny did not drop earlier, but the principal cause must be the huge gap in communication that exists between anthropology, especially social anthropology, on the one hand, and the humdrum world of population and statistical genetics on the other. When someone like Lewontin bridges the gap, bearing from genetics a message which the other side wants to hear, it spreads fast – on that side. But there was no feedback. Others might have noticed Lewontin’s 1972 paper but I had stopped working in human and population genetics in 1968 on moving to Cambridge because I could not get any support (so I settled down to writing books instead). In the 1990s I began to pick up the message about only 15% of human genetic variation being between, as opposed to within, populations with its non-sequitur that classification was nigh impossible, and started asking my population-genetics colleagues where it came from. Most had not heard of it, and those that had did not know its source. I regret now that in my paper I did not acknowledge the influence of my brother John, Professor of Genetics in Oxford, because he was independently worrying over the question, inventing the phrase ‘the death of phylogeny’ which spurred me on.

Eventually the argument turned up unchallenged in Nature and the New Scientist and I was able to locate its origin. I only started writing about it after lunch one day in Caius during which I had tried to explain the fallacy across the table to a chemist, a physicist, a physiologist and an experimental psychologist – all Fellows of the Royal Society – and found myself faltering. I like to write to clear my mind. Then I met Adam Wilkins, the editor of BioEssays, and he urged me to work my notes up into a paper.

I have had no adverse reaction to it at all, but plenty of plaudits from geneticists, many of whom told me that they too had been perplexed. Perhaps the communication gap is still too large, or just possibly the point has been taken. After all, Fisher made it in 1925 in Statistical Methods which was written for biologists so it is hardly new. [my emphasis -R]

Richard Dawkins repeated Edward’s argument in The Ancestor’s Tale. You can read Edward’s full essay online. Also see p-ter’s lucid exposition at GNXP.

discblogsSo far I’ve been talking mostly about genes. But in terms of classification there isn’t anything magical about genes. Biological anthropologists using more robust morphometric traits have discerned an “Out of Africa” movement, just as geneticists have. You have above five individuals. All of them have dark hair and dark eyes. There’s total overlap on those traits. And yet I’m pretty sure you can assign their rough population identity to each. Why? Because humans take a look at correlated clusters of traits in assigning population identity intuitively. Some traits are more salient, such as skin color, but early geographers understood that East Asians and Europeans were different populations despite similarity of light complexion. The ancient Greeks understood that Indians and Ethiopians were different groups despite their similar complexions, because they differed on other informative traits.

Let’s bring it back down to earth. Population structure exists. Phylogenetic analyses of humans are trivial in their difficulty. They track geography rather closely, at least before the age of mass migration. Additionally, they tend to follow endogamous social groups, such as Ashkenazi Jews. A South Asian is going to be more genetically related to a South Asian than they are to an African. There are many cosmetic differences between populations. But there are also less cosmetic differences which are very important. You can even assign different regions of a chromosome to different ancestral components.

Where does this leave us? Ultimately, it’s about the “R-word.” “Race is a myth.” Or, as PBS stated, an illusion. Here’s some of the precis of the PBS documentary:

Everyone can tell a Nubian from a Norwegian, so why not divide people into different races? That’s the question explored in “The Difference Between Us,” the first hour of the series. This episode shows that despite what we’ve always believed, the world’s peoples simply don’t come bundled into distinct biological groups. We begin by following a dozen students, including Black athletes and Asian string players, who sequence and compare their own DNA to see who is more genetically similar. The results surprise the students and the viewer, when they discover their closest genetic matches are as likely to be with people from other “races” as their own.

Much of the program is devoted to understanding why. We look at several scientific discoveries that illustrate why humans cannot be subdivided into races and how there isn’t a single characteristic, trait – or even one gene - that can be used to distinguish all members of one race from all members of another.

Modern humans – all of us – emerged in Africa about 150,000 to 200,000 years ago. Bands of humans began migrating out of Africa only about 70,000 years ago. As we spread across the globe, populations continually bumped into one another and mixed their mates and genes. As a species, we’re simply too young and too intermixed to have evolved into separate races or subspecies.

So what about the obvious physical differences we see between people? A closer look helps us understand patterns of human variation:

  • In a virtual “walk” from the equator to northern Europe, we see that visual characteristics vary gradually and continuously from one population to the next. There are no boundaries, so how can we draw a line between where one race ends and another begins?
  • We also learn that most traits – whether skin color, hair texture or blood group – are influenced by separate genes and thus inherited independently one from the other. Having one trait does not necessarily imply the existence of others. Racial profiling is as inaccurate on the genetic level as it is on the New Jersey Turnpike.
  • We also learn that many of our visual characteristics, like different skin colors, appear to have evolved recently, after we left Africa, but the traits we care about – intelligence, musical ability, physical aptitude – are much older, and thus common to all populations. Geneticists have discovered that 85% of all genetic variants can be found within any local population, regardless of whether they’re Poles, Hmong or Fulani. Skin color really is only skin deep. Beneath the skin, we are one of the most similar of all species.

Certainly a few gene forms are more common in some populations than others, such as those controlling skin color and inherited diseases like Tay Sachs and sickle cell. But are these markers of “race?” They reflect ancestry, but as our DNA experiment shows us, that’s not the same thing as race. The mutation that causes sickle cell, we learn, was passed on because it conferred resistance to malaria. It is found among people whose ancestors came from parts of the world where malaria was common: central and western Africa, Turkey, India, Greece, Sicily and even Portugal – but not southern Africa.

This documentary came out in 2003. In late 2005 scientists discovered the role that SLC24A5 plays in skin color. It is the second most ancestrally informative locus typed so far to differentiate Europeans and Africans. It actually does come close to being a single gene which differentiates two populations! It is true that human populations have mixed. I probably have ancestors who were resident in China and Northern Europe within the last 1,000 years. That’s the way genealogy works. All Eurasians may be able to find a genealogical line of ancestry back to Genghis Khan (though not necessarily distinctive genes attributable to him). But that does not negate the fact that some of your ancestors show up in your pedigree orders of magnitude more than others of your ancestors. The vast majority of my ancestors within the last 1,000 years were South Asian, though a substantial minority were Southeast Asian. The question of our youth as a species and its relation to our differentiation into races and subspecies is an empirical matter, not an a priori one determined by a fixed number of years. Since races and subspecies are fuzzy characteristics they’re easy to refute, just pick the definition which is refutable. I have no idea how they adduce that traits like intelligence, musical ability, and physical aptitude, are that much older than the “Out of Africa” migration. Humans have been getting much more gracile over the last 10,000 years as a whole, while I don’t know how one can know about the musical abilities of anatomically modern humans in Africa 200,000 years. These traits are quantitative, and based on standing genetic variation, so the architecture is qualitatively different from that of skin color (though in 2003 we didn’t know the architecture of skin color, the confusion is explainable).

The old concept of “race” as outlined by anthropologists in the early 20th century, and accepted broadly, was often unclear, ad hoc, and not empirical. Over the past generation by way of refuting the concept of race people are wont to make unclear, ad hoc, and non-empirical, assertions. The reason that scholars discuss race and refute it is to eliminate confusions and misconceptions from the public, but their presentation has produced more confusions and misconceptions. The idea that human phylogeny is impossible is in the air, I have heard it from many intelligent people. I have no idea why people would be skeptical of it, the way it is presented by many scholars makes the implication clear that phylogeny is impossible, that differences are trivial. Both these are false impressions. I do not believe that the fact that mixed-race people’s real problems obtaining organs with the appropriate tissue match is a trivial affair. Human genetic differences have plenty of concrete impacts which are not socially constructed.

Personally I have no problem with abandoning the word race and all the baggage which that entails. But there’s no reason to throw the baby out with the bathwater here. In the “post-genomic” era human population substructure is taken for granted. The outlines of the history of our species, and its various branches, are getting clearer and clearer. There’s no point in replacing old rubbish with new rubbish. We have the possibility for clear and useful thought, if we choose to grasp it.

  • Larry, San Francisco

    One thing I have always been curious about is East Africans (Nilotic, Sudanese, Ethiopian) relation to West Africans (who I think are mainly Bantu) and Arab, Mediterranean people. The East Africans do look different from West Africans and I believe there was a lot more interaction with Mediterranean people historically. I looked at some of the African groups on your graph and the only group that I could find that was East African were the Luhya who are Bantus.

  • http://blogs.discovermagazine.com/gnxp Razib Khan
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  • Billare

    I just don’t understand how very intelligent, very competent scientists can tolerate the current atmosphere and not feel intellectually stifled. I’ve only been really getting into anthropology, evolutionary genetics and such for about 2 years, and that you’ve said here clicked very easily for me within hours of reading AWF Edwards’ paper. If I can be a naif compared to you and Dienekes and other serious bloggers and feel wronged by the trash they teach as the current consensus how can others not be?

    There are at least 2 other ideas I think make Lewontin’s F_ST calculation virtually useless for forwarding the political conclusions the anti-racists want to draw from it:

    1. When the word “race” is used in the United States, operationally, it’s used for populations that had quite a bit of genetic distance and barriers to gene flow between them: European-Americans African Americans, and perhaps Euro-Americans/Native Americans. So there were was plenty of time for genetic drift to operate, increase intra-population variation, and produce the genomic correlations that lead to concordant phylogenies — which goes against the argument that one could produce a multiplicity of racial classifications depending on which genes/phenotypic characters one chooses, not for the groups usually implicated in American sociopolitical controversies, anyway. E.g. the separation between Africans/non-Africans is always the first component of variation to fall out, and the E-W Eurasian divide the second, with enough randomly chosen alleles chosen.

    2a. Effect size matters. The example that always comes to mind for me is when you mentioned somewhere that Khoisan Bushmen from neighboring villages can show deep splits in mitochondrial (and presumably other neutral) DNA while maintaining remarkably similar appearance. That implies the F_ST between African populations can be practically unimportant as long as both are exposed to the same selective pressures. And similarly, even small F_ST between human populations could imply radical behavioral differences in the face of strong selection.

    2b. We often care alot more about our differences than our similarities. Most human beings walk bipedally, use tools and language, which the authorities have informed me are radical departures from our LCA with chimpanzees. But despite relatively trivial differences between my DNA and say, Lebron James’, he’s still making many hundreds of millions of dollars more than me. Even if human biodiversity were less than it were we’d still have “racial” controversy as long as those differences were systematic between populations and not randomly distributed within them.

  • vineviz

    I’m having a hard time figuring out what point razib is trying to make in this post.

    Is it really simply that it is possible to classify humans? It appears so, but that’s baffling for two reasons: 1) I’m not aware that anyone was making the counterpoint; and 2) the fact that we ability to classify humans does not serve as evidence that biological races exist.

    Take his lead example. Surely, anyone can see that it is possible to classify humans into categories based on their values at rs1426654. But that is WAY beside the point.

    Would razib have us believe that rs1426654=AA is one race, while rs1426654=TT is another race? Surely he would not.

    Besides, how would such a racial classification system handle someone who is heterozygous (i.e. rs1426654=AT)? And at the population level, what is the point where in west Asia is the ratio of A:T become “European”? And why build a racial classification scheme on this particular SNP, when another SNP would sort people differently? Isn’t the decision to focus on rs1426654 somewhat arbitrary? I’d argue that it is.

    But this is a tired argument. I think that failure of race-defenders to offer up a clear and defensible definition of race in which it is a non-arbitrary biological construct is where the debate SHOULD end.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    vineviz, did you bother reading my links? if you’re tired, don’t post again. seriously.

  • http://johnhawks.net/weblog John Hawks

    So here’s my question. We all know now that people tend to tilt their heads to the right to kiss. Yet all the science bloggers pictured here are tilting their heads to the left.

    All, that is, except for one…

  • vineviz

    Yes, I read your links (the ones I had not read many times before, that is). Your point?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    let me make it explicit: don’t comment here anymore. i spent over 2,000 words on “my point.” if you don’t get it, that’s fine.

  • http://washparkprophet.blogspot.com ohwilleke

    Yes, it “race” defined as non-arbitrary large scale clusters of genetically similar individuals exists, and is well defined for a large share of the population. But, ancient continental racial distinctions are better defined in some places than others. In Europe, most of Sub-Saharan Africa and East Asia, almost everyone fits neatly into a continental racial cluster, and further into very finely graded subclusters as distinct as individual islands, villages and valleys.

    In the United States, a very small portion of the nation lives in places where the very fine graded subclusters exist as anything more than statistical flukes, and a very large proportion of the population doesn’t fit exclusively in a single continental racial cluster. A disproportionate number of Americans (relative to other places) fit in the gaps between the clusters on the neat chart above. We are not the easiest place to sort.

    About 1.8% of American identify as mixed race generally from admixture in the last generation or two, and a very large share (probably in excess of 90%) of Americans who identify as African-American (12.9% of American), Native American (1.0% of Americans), and Hispanic (16.0% of Americans) have significant European ancestry admixed with African and/or indigeneous American ancestery. Some people who identify on census forms as white or Asian also don’t belong to the plurality continental race of people who make that identification (either due to admixture, or because a category includes more than one such category — hence an Aboriginal Australian and a Han Chinese person and a Telagu speaker from India are all Asian and Pacific Islanders in the census). Thus, it is fair to say that more than 28% of Americans don’t even fit neatly into one of the continental racial boxes on the PCA component 1 and 2 charts, and the trend is clearly for this share of the American population to grow (e.g. outmarriage rates of Asian American, Hispanic and Jewish women approach 30%-50% and are higher among those with college educations, and exceed 10% for African-American women). The extent of admixture, moreover, varies significantly both within and between subgroups of the conventional racial classifications used in the United States.

    The other important point that calls for caution is that one of the primary reasons for intuitive racial classification by ordinary people is to infer ethnicity and socio-economic status, not as an end in its own right. Ethnicity is a cultural cluster in which language and religion play particular important parts and has many other components. But, the link between ethnicity and socio-economic class, which are often more important in social and business interactions than race, with race, is weakening. Every middle class American knows a racially Asian American child adopted at a very early age who is ethnically white. Growing immigrant populations from Africa in the United States (mostly Ethiopian and Somolian in my neck of the woods in Denver) are ethnically distinct from African-Americans. An Arab looking person is more likely to be Christian than Muslim in most of the United States, due to immigration patterns, despite the trends in their countries of ancestral origin. Most white Americans have an ethnicity that is far more Anglo than their European ancestors. For practical purposes, the average person needs dozens of race-ethnicity-socio-economic class combinations to make useful at a glance inferences about people, not a count on your fingers set of continental racial groupings.

    Extreme caution about using racial classification as a valid tool in the United States is appropriate given, (1) the far greater than average ambiguity of race (understood in a scientifically accurate way) in the United States than most places, (2) substantial disconnect between folk race definitions and genetic clusters, (3) the growing inaccuracy of ethnic and socio-economic inferences derived from race in the United States, (4) the history of race relations in the United States that present a plausible historical environmental cause rooted in folk racial classification for almost any distinction relevant to day to day life or economic or legal considerations that exists between races, that parallels any genetic distinction and makes separating out the two difficult, and (5) a history in which folk racial classifications have been used when legitimatized for purposes where no racial classification is appropriate.

    For medical diagnostic purposes, genetic testing for particular relevant genes is usually going to be more accurate than racial classification, although few people worry about medical doctors using race as one factor of many in making medical diagnosis.

    The big concern is about using inferences based on race in law enforcfement, employment, social interactions and public services where the link between anything genetic is far more attunated, even if it is statistically significant, because this is sufficiently inaccurate that this practice functions as social acid dissolving any kind of consensus civility or support for a common society.

  • dan

    razib, do you think these types of errors in type II thinking are mostly genetic? it really seems to me that no matter what you tell certain people they are not going to simply rely on raw data but will interpret it in their own way or find data that agree with their world view. is this how high IQ people end up being religious (apart from the obvious influence of how they’re raised)? many people simply don’t have the gumption to allow the data to speak for itself if it seems to point to something unpleasant. i don’t think i know more than a couple of people who are truly willing to just “let go” and and be a true empiracist.

  • JL

    Edwards was not the first to make the Lewontin’s fallacy argument. As pointed out in the Wiki article, Jeffry Mitton argued the same point in the 1970s:

    * Mitton, Jeffry B. (April 1977). “Genetic Differentiation of Races of Man as Judged by Single-Locus and Multilocus Analyses”. The American Naturalist 111 (978): 203–212. doi:10.1086/283155.
    * Mitton, Jeffry B. (1978). “Measurement of Differentiation: Reply to Lewontin, Powell, and Taylor”. The American Naturalist 112 (988): 1142–1144. doi:10.1086/283359.

    Steve Hsu has posted early PCA maps of human genetic differentiation by Cavalli-Sforza and Mitton here: http://infoproc.blogspot.com/2009/06/genetic-clustering-40-years-of-progress.html

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    luke jostins has a valid criticism on the lack of clarity in my post:

    http://twitter.com/lukejostins/status/14820079908683777

    my response: probably should be an article, not a blog post i write up in a few hours on the spur-of-the-moment. so i’ll try and put something together that’s more clear and precise when i have more time. perhaps a few weeks.

  • vineviz

    Razib, it’s my observation that you spent over 2,000 words without making a point. Perhaps you’d be well served by using fewer, better chosen words?

    Against my better judgement, I’ve read the post again and I reach the same conclusion I did earlier, which is that your position is in essence synonymous with those you profess to disagree with: human variation exists, that variation is important, and that variation does not validate “race” as a biological reality.

    I don’t blame you for disliking my observation, by the way, but I will make one more observation: I don’t hold much respect for bloggers who restrict comments to sycophants. If that’s not your policy, I hope you’ll say as much.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    ohwilleke, i think you overestimate the power of admixture in this case. though almost all african americans have some recent admixture of european ancestry, 90% is less than 50% european. this means that though AA don’t form a tight cluster, they exhibit a tendency to be along a linear distribution between their two parent populations, with a skew toward africans. e.g.,

    http://blogs.discovermagazine.com/gnxp/2010/05/genetic-variation-among-african-americans/

    the stuff about social construction is real. i obviously don’t dispute that, and i’ve pointed to it myself. my point though is that too often there is an confounding of the social construction of racial categories, and, the emergence of population structure from genes in the data. the latter often exhibit clear and distinct patterns.

    in fact, i have argued before that if you weight the variation in allele frequency as a function of population in a given area, it would give you a better sense of the discontinuous aspect of some clines. there are only ~10 million uyghurs. there are 500 million europeans and 1.3 billion han.

    i don’t think i know more than a couple of people who are truly willing to just “let go” and and be a true empiricist.

    this is a huge human problem. periodic switches into epoche are useful:
    http://en.wikipedia.org/wiki/Epoch%C3%A9

  • http://blogs.discovermagazine.com/gnxp Razib Khan


    I don’t blame you for disliking my observation, by the way, but I will make one more observation: I don’t hold much respect for bloggers who restrict comments to sycophants. If that’s not your policy, I hope you’ll say as much.

    1) i don’t give a shit what you think. there are a few dozen regular commenters whose opinions i value. the rest of you are not too important because you aren’t invested. reading blog posts is a grace which you have utmost liberty to do. leaving comments is a privilege which i yank away constantly.

    2) my policy is to discourage comments which aren’t useful in furthering discussion. any discussion between you and i is at an impasse so that’s why i encourage you not to engage me. if you want to elaborate in a blog post if you have a blog to post on, or even in a long comment, go ahead. i’m not inclined to spend more time responding to short queries because the post was my response to you.

    3) i gave you a little more credence than the other random commenters because i looked you up (your email is connected to your FB), and you obviously know genetics (and assume know how factor analysis/PCA works, going by your undergrad degree), so i thought that i could clear up confusion. obviously it didn’t happen, and i doubt we have the time or energy to go any further. the disagreements are upstream.

  • dan

    re: epoche

    nice. thanks for the link

  • Antonio

    Just a minor point on the social aspect of it: OK, it is not hard to classify humanity and, perhaps, this could be useful or even needed. However, h0w to avoid the hierarchies that follow these classifications? You know, if you’re different from me someone must be the best one. One way to preclude this – or at least one way that science could *not* help the formation of such hierarchies – might be via avoiding global classifications, such as race. Instead we could focus on classifications over particular traits. Perhaps…

  • http://lyingeyes.blogspot.com ziel

    ohwilleke: Extreme caution about using racial classification as a valid tool in the United States is appropriate…
    Antonio: One way to preclude this…might be via avoiding global classifications…

    Suppose we proposed an across-the-board rule in the United States that racial classifications shall never be used anywhere in the country forevermore as a basis for decision making in any endeavor…how do you suppose the voting on that rule would fall along existing racial classifications?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Just a minor point on the social aspect of it: OK, it is not hard to classify humanity and, perhaps, this could be useful or even needed. However, h0w to avoid the hierarchies that follow these classifications? You know, if you’re different from me someone must be the best one. One way to preclude this – or at least one way that science could *not* help the formation of such hierarchies – might be via avoiding global classifications, such as race. Instead we could focus on classifications over particular traits. Perhaps…

    ppl do this all the time already. you think phylogenetics makes a big difference? i don’t. anyway, ppl look at the same data, and draw opposite conclusions. both zionists and anti-semites find validation in the jewish genetics posts.

  • Jeff

    ” However, h0w to avoid the hierarchies that follow these classifications? You know, if you’re different from me someone must be the best one. One way to preclude this – or at least one way that science could *not* help the formation of such hierarchies – might be via avoiding global classifications, such as race. Instead we could focus on classifications over particular traits. Perhaps…”

    I think this is too paternalistic. Scientists are not and should not be the gatekeepers of knowledge, even the thought of this is pretentious and hierarchical in itself.

    If people want to make generalizations and condemn others simply based on some ancestral event, its their loss.

  • MK

    ***Edwards was not the first to make the Lewontin’s fallacy argument. ***

    Peter Frost also points out another possible issue with Lewontin’s finding:

    “3. The way a gene varies within and between populations will itself vary as a function of the gene’s selective value

    When genes vary between populations, they do so usually because the population boundary separates different environments with different sets of selection pressures. Genes that differ across this boundary are necessarily genes that make a difference, i.e., that have high selective value.

    In contrast, selective value is necessarily low for genes that differ within a population despite similar selection pressures (unless the different variants form a balanced polymorphism).

    The two kinds of genetic variation are therefore not comparable.”

    http://evoandproud.blogspot.com/2010/09/evolution-of-cavalli-sforza-part-iv.html

  • Antonio

    “I think this is too paternalistic. Scientists are not and should not be the gatekeepers of knowledge, even the thought of this is pretentious and hierarchical in itself.” I think this is too naive :)

    PS: what’ is ppl? I google it but I’m not sure. Sorry for the ignorance. Thank you,

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    antonio, it’s a moot point. anyone can download EIGENSOFT and ADMIXTURE. even if researchers started gating off HGDP and HapMap, you could do something like dodecad.

    so what do you propose would just result in amateurs doing all the research & analysis. it’s not that hard now.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    readers might find the digg comments amusing.

  • http://www.iSteve.blogspot.com Steve Sailer

    Leaving aside all the politics, the fundamental epistemological shortcoming of most thinking about race is that the vast majority of intellectuals think about race as involving Linnaeun species writ small rather than as extended families writ large.

    If you think of racial groups as “partly inbred extended families,” you’ll suddenly find that your thinking becomes much more productive.

    If you’ve never thought about race this way, please try it.

  • Andrew Lancaster

    Vineviz wrote: “I’m having a hard time figuring out what point razib is trying to make in this post.”

    Vineviz, I see Razib define the fallacy as “the claim that human geographical races have no biological meaning”.

    I guess, based on the blog post that led to this one, that Razib has in mind a kind of of person who claims that the human races can not be recognized at all by biologists in any clear logical way, or something like that. Such people would indeed be wrong. Using genetics we can divide up humanity into many populations, indeed many more than anything like the normal concept of races, but something like the traditional races would I think normally be recognizable as one level of categorization?

    To me, and I guess you, a more important thing to discuss is whether the biological meaning of the human races is the same as what people normally mean when they speak of races. Razib seems to see it that way also. I guess your point is that you are not sure what his conclusion is about this.

    In effect what some people think, and I guess that Razib is also playing with the idea based on the top graph, is that the races as normally understood are more clearly defined than any other level of human clustering we can do.

    Although that top graph makes it look that way I am not sure it should be understood that way. It is not a sampling of continuous neighbouring populations to begin with, so it would be expected to show some big gaps between regions. It does show, unsurprisingly, that genetic distance is not the same as geographical distance, but that is not quite the same as what is being discussed I guess?

    Razib, I’ll stop at that, because you did not like my previous posts. : D But I’d honestly be interested to know if I am understanding you correctly?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Razib, I’ll stop at that, because you did not like my previous posts. : D But I’d honestly be interested to know if I am understanding you correctly?

    basically.

    i believe that species can still be instrumentally useful as a term for organizing phylogenetic relationships even amongst promiscuously hybridizing clades. so obviously i’d think that something race-like is useful as a classification term.

  • Andrew Lancaster

    “i believe that species can still be instrumentally useful as a term for organizing phylogenetic relationships even amongst promiscuously hybridizing clades. so obviously i’d think that something race-like is useful as a classification term.”

    I would have thought that of all the surviving names for different types of clade, “species” was one of the stronger ones. I know there are exceptions, but generally I’d have thought a species will be a more easy-to-define category than a race or sub-species? Actually, in a sense I guess some people would say that by definition a species should be understood as the lowest level of really clear distinction between a population and its closest relatives, or to put it maybe the lowest level of population distinctiveness which is also distinctively more distinct than just any old distinctiveness. For example different species tend not to interbreed and so on.

    Would agree that a species will normally be more distinctive than a sub-species?

  • Jason Malloy

    The annoying thing about these race “debates,” is that the race “skeptics” think that their verbal assertions about the scientific uselessness of the race concept can somehow outweigh the reality on the ground: scientific paradigms are only as real as their usefulness to scientists, and biological race is a ubiquitous paradigm in science in both name and concept.

    For example, let’s take, I dunno, say anthropology:

    Of the 810 articles on modern human variation published in the AJPA during the years sampled [1965-1996], 40.5% utilized racial categories… the role played by racial taxonomy in the study of modern human variation has apparently changed little or not at all over the course of the past 30 years.”

    Boy, it’s a lucky thing we have cultural anthropologists around to make empty verbal arguments about the worthlessness of paradigms that actual productive scientists create cited research material around. Otherwise one might mistakenly think that the usefulness of scientific paradigms was demonstrated by this process of usage and content generation instead of by ex cathedras and insular verbal exercises.

    And this is their own discipline! The “most powerful [contribution] to the public understanding of humankind” cultural anthropologists have made is to grossly misrepresent the applied realities of the science going on in their own discipline (much less across the full spectrum of biological disciplines).

    You’ll find the same importance of race in almost every scientific discipline associated with human biology, and equally ubiquitous critics on the sidelines reminding these scientists, Morpheus-like, that they’re all swimming in the same grand shared illusion. Recall Robert Schwartz’s arrogant, clueless NEJM editorial that race was somehow a popular variable in bio-medical research despite being a “biologically meaningless” “pseudoscience”:

    ““race” is biologically meaningless”… [yet] race-based medical research is widespread. The pseudoscience of race is well represented in clinical investigations. In March 2001, under the search term “Negroid race,” Medline contained 13,592 citations, of which 1301 appeared in 1999 or 2000 … Such research mistakenly assumes an inherent biologic difference between black-skinned and whiteskinned people.”

    Well QED. They must be biologically identical if most bio-medical researchers are treating them like they are biologically different. Your assertion here is extremely valuable – much more than all these measurements, experiments, and statistics.

  • vineviz

    Jason said scientific paradigms are only as real as their usefulness to scientists, and biological race is a ubiquitous paradigm in science in both name and concept.

    There are very few papers being published by geneticists which use the term “race” or even defend the concept. Did you see the recent review by Barbujani et al. on human genome diversity? E.g. “It is unclear whether there might be practical advantages in describing humans as if they were divided into biological races, even though we know they are not.”

    But of course scientists classify organisms (including humans) all the time: they do so because classification is useful and convenient. No one, not even “race skeptics” suggest otherwise. Rather, it seems the skepticism seems to be stirred up by the notion that there exist some fixed number natural of natural groups, for which all locii are essentially homogenous within but heterogenous between groups. If genetics has told us anything, it has told us that.

    Barbujani again: “As a consequence, we can cluster people based on any set of polymorphisms, but there is no guarantee that the same clustering will be observed when considering other polymorphisms in the same individuals. “

    Now, in the end I know that razib is not contradicting this. Certainly nothing in this blog post contradicts it. To the extent that I can speak for informed race “skeptics” (because that’s what I consider myself) it’s that we must avoid being fooled into thinking that clustering by polymorphisms is a support for the traditional notion of racial categorization.

  • Jon

    I used to demo the PCA of the HapMap data during SNP analysis training sessions. Lots of fun for people that hadn’t seen it before.

    Just wait until they get more/better indel data and we’ll be even more separable.

    vineviz, I am a little confused what you consider the ‘traditional notion of racial categorization’. I’d say the categorization is fine, even in a traditional sense we usually do OK. The only thing that is changing (and rightfully so) is what we assume the categories mean.

    For example, let us take sex. We are, for the vast majority, perfectly fine with traditional boundaries of sex. We have only evolved how we stereotype based on the category. So too with race, the only thing that needs evolving is how we react and interpret, not how we categorize.

  • dan

    vineviz – you’re saying the equivalent of saying that there are no such thing as dog breeds. why are you such a science denier? are you religious?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Would agree that a species will normally be more distinctive than a sub-species?

    sort of. though it seems that ‘species’ as we understand it is cladocentric. it is less useful for groups of plants which hybridize like crazy, or clonal lineages.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Rather, it seems the skepticism seems to be stirred up by the notion that there exist some fixed number natural of natural groups, for which all locii are essentially homogenous within but heterogenous between groups.

    if someone knows what a locus is, and can spell heterogeneous, they won’t accept such an extreme scenario.

    “As a consequence, we can cluster people based on any set of polymorphisms, but there is no guarantee that the same clustering will be observed when considering other polymorphisms in the same individuals. “

    if you take a large number of a random set of loci, the same clusters DO reemerge. people use different SNP-chips, they use microsatellites, they use indels. as long as the N of the markers is large enough you see clusters reflecting evolutionary history.

    basically, i think humans do shake out into non-arbitrary and exclusive clusters.

  • Jason Malloy

    “There are very few papers being published by geneticists which use the term “race” or even defend the concept.”

    Geneticists have no more need to ‘defend’ race than a fish needs to defend water: they’re both swimming it. Racial categorization is so fundamental to (indeed, in some ways synonymous with) the practice of population genetics, that I can’t imagine how population genetics would verbally communicate or verbally express their discipline without it. Genetics papers across all the various sub-disciplines routinely describe and analyze groups of people by hierarchical labels of commonly recognized (and empirically verifiable) ancestry groupings: Eurasians, Sub-Saharan Africans, West Africans, Northern Europeans, Jews, Italians, blacks, whites, etc. This classification by ancestry grouping is exactly what race is, and what it has always signified to biological scientists: scientifically useful population identity within and below the level of species.

    “Rather, it seems the skepticism seems to be stirred up by the notion that there exist some fixed number natural of natural groups, for which all locii are essentially homogenous within but heterogenous between groups. If genetics has told us anything, it has told us that.”

    This is a bizarre and ahistorical conceptualization of race with no relevance. In the 1970s Richard Lewontin first argued that greater genetic differences within groups than between groups obviated the need for racial classification. But this does not mean that racial groupings were ever understood as the obverse. ‘Negroid’ meant the same thing to pre-Mendelian Charles Darwin as it does to the post-Mendelian bio-medical researchers criticized above: people with shared hereditary traits of sub-Saharan African ancestry.

  • http://washparkprophet.blogspot.com ohwilleke

    Medline contained 13,592 citations, of which 1301 appeared in 1999 or 2000

    This is largely a function of easy availability of data (i.e. looking for your lost keys under the streetlight rather than in the dark alley where you think you probably dropped them). It is far easier to use data that are already collected by someone else in the ordinary course, even if they are less than ideal, than it is to collect new data of your own. Religious denomination affiliation and male surnames are quite a good proxy for genetically distinct populations among American whites (and even better if reporting of those criteria about people’s parents by subjects are used and there is a filter by geographic place of origin of one’s parents in close cases), probably almost as accurate as race, yet this data isn’t routinely collected and so it isn’t routinely considered in medical studies.

    “almost all african americans have some recent admixture of european ancestry, 90% is less than 50% european”

    The mean is on the order of 25% European in African Americans (FWIW, I dislike the acronym AA for “African American” because that was the acronym for “Asian American” and never used for “African-American” until I was in my 30s and now has become ambiguous in either sense).

    Also, the functional and legal “one drop rule” in folk racial classification makes the argument that folk racial classification is very solidly connected to genetic classification weak. Given the possibility of confusion between the two sense of the word that are false friends, and the far more limited community of people who use the term race to mean “genetically similar clusters,” should be disfavored in the scientific community in favor of terms like “genetiically similar clusters” or the less clunky “populationns” with geographical or ethnic qualifiers (e.g. “West Eurasian populations”).

    Suppose we proposed an across-the-board rule in the United States that racial classifications shall never be used anywhere in the country forevermore as a basis for decision making in any endeavor…how do you suppose the voting on that rule would fall along existing racial classifications?

    This is the law in quite a few American states (with the caveat that “any endeavor” does not include marriage/dating decisions of individuals themselves and a handful of other highly personal areas where enforcement would probably be futile anyway). Where it has been put to a vote is has received wide support in all existing racial classification categories, although there has been a partisan divide (with politically aware liberals favoring continued affirmative action). Of course, any action to enforce such a law would have to have some way to document that decision making was made on that basis and a suit for violation of that law would be “an endeavor.”

  • http://www.kinshipstudies.org German Dziebel

    ““As a consequence, we can cluster people based on any set of polymorphisms, but there is no guarantee that the same clustering will be observed when considering other polymorphisms in the same individuals. “

    if you take a large number of a random set of loci, the same clusters DO reemerge. people use different SNP-chips, they use microsatellites, they use indels. as long as the N of the markers is large enough you see clusters reflecting evolutionary history.

    basically, i think humans do shake out into non-arbitrary and exclusive clusters.”

    Razib is right, Vincent is wrong. With one locus, cluster boundaries are fuzzy, with multiply loci they are more solid and keep recurring no matter what loci you throw into the mix. As the quoted paper by Barbujani & Colonna says, “Populations are indeed structured in the geographical space but, when it comes to predicting individual DNA features, labels such as ‘European’, ‘Asian’ and the like are misleading because members of the same group, Watson and Venter in this case, can be very different.” Again, racial labels work well for populations, less so for individuals. The problem is how those clusters emerged, what is the course of our evolutionary history and, as somebody rightly pointed out, how do we act on those differences in the future. The fact that geneticists highlight African intragroup diversity and interpret that diversity as a sign of age is problematic. Intergroup diversity in Africa is lower than in places like Oceania and America, and it is in those latter regions that our old Pleistocene demography is likely manifested. These are also the areas that contain the largest fraction of the proverbial 15% of intergroup variance characteristic of our species. This means that the earliest stages of our species-building differentiation occurred way outside of Africa. So, the denial of the biological reality of geographical clusters goes hand in hand with the desire to portray our evolutionary history as progressive loss of intragroup variation from the African cluster to the Amerindian cluster and the accumulation of intergroup variation through bottlenecks. The reality seems to be the opposite: the progressive replacement of original Pleistocene demes/micro-races by large expansive Asian, African and European clusters.

  • Andrew Lancaster

    Razib: sort of. though it seems that ’species’ as we understand it is cladocentric. it is less useful for groups of plants which hybridize like crazy, or clonal lineages.

    Fair comment. Will keep in mind when plants come up. :D

    Jason: Racial categorization is so fundamental to (indeed, in some ways synonymous with) the practice of population genetics, that I can’t imagine how population genetics would verbally communicate or verbally express their discipline without it.

    I think it is more useful to home in on what is really controversial. No one is really denying such categorization is part of biology I think. It is whether biologists call categories of populations smaller than a species a “race” normally. They don’t, and I think choosing words is not just something we do at random. There is a reason they don’t. The word has (to use Razib’s term) baggage.

    GD: if you take a large number of a random set of loci, the same clusters DO reemerge

    Yes. I think Vineviz unintentionally implied otherwise. But do you accept that the same individuals can be in many different significant clusters at once, when you do this kind of analysis?

    Dan: vineviz – you’re saying the equivalent of saying that there are no such thing as dog breeds.

    Dog breeds and other domestic animal races are the one area where biologists probably do refer to races. It is interesting to consider whether there is any special characteristic of domestic races which justifies using a different word than biologists use for other animals. In fact, there are some interesting characteristics. These animals do not just live in fuzzily defined populations that interbreed to varying extents. They are the result of deliberate breeding programmes and this has an effect on how their offspring share in their characteristics. Do these special conditions apply to man?

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Do these special conditions apply to man?

    i think humans are ‘self-domesticates.’ not only that, i think we’re affected more by the domesticates we are associated with than we realize (cow milk is obvious, but what about toxoplasmosis?).

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    also, let me clear something up: i’m not that invested in the word ‘race.’ i’m interested in patterns of human variation, similarity, and population structure. the way that race-is-a-myth is taught in american society often results in total miscomprehension of the reality of these patterns, or the ability to discern them. e.g., The Inconvenient Science of Racial DNA Profiling.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    btw. this argument kind of reminds of arguments of how to define a ‘planet.’

  • vineviz

    @ German Dziebel : With one locus, cluster boundaries are fuzzy, with multiply loci they are more solid and keep recurring no matter what loci you throw into the mix.

    Sorry, but that’s not true at all.

    What appear to be “solid” boundaries in the PCA plots you are used to observing in papers is simply an artifact of sparse sampling. If you sample just two distant populations (say, one small village in southern Italy and another in northern Finland) you may indeed be able to concoct a PCA or cluster analysis that will result in 100% of the Italians in one group and 100% of the Finns in the other. As razib might say, it’s “not that hard”.

    But if, instead, you sample villages at small intervals (e.g. 10km or 50km) along that entire axis you’d end up with a different picture altogether: one in which there is no obvious place to draw a line between southern Europe and northern Europe. Do the same between Chad and Iraq, and you’ll get the same conundrum: no obvious place where -absent some social or historic override – the is a clear line between Asian and African. That is NOT the same as saying that Iraqis and Chadians are somehow the same. It IS saying that they are just two points on a continuum (or, even better, on a large number of continuums).

    Even in the O’Dushlaine paper razib links above, you have to introduce social filters (4 grandparents from the same village, control for inbreeding, etc.) to get even the weak effect they highlight.

    This matters because, despite remarks to the contrary above, the typical racial classification schema do imply a clean phylogenetic relationship in which intraracial relationships are stronger than interracial relationships. But the science simply doesn’t bear this out.

    Which is why geneticists have, indeed, largely abandoned the concept of “race” in favor of more precise and more accurate classification schemes. I agree with razib, in that study and analysis of human genetic variation is very interesting and not-at-all fruitless. That doesn’t change the fact that race is, in the end, a social construct and that “social construct” is not a synonym for “useless”.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    This matters because, despite remarks to the contrary above, the typical racial classification schema do imply a clean phylogenetic relationship in which intraracial relationships are stronger than interracial relationships.

    we already established Fst on the order of 0.15 is the high bound. yes, stupid people may look at a tree and forget abut intra-pop variance or the reticulation which is elided, but non-stupid people have already discounted that. a significant minority of the world literate population still remains reflexively geocentric. i’m not talking to those ppl.

    It IS saying that they are just two points on a continuum (or, even better, on a large number of continuums)

    even classical cladistics focusing on shared derived trades often imposes a technically false model where there hasn’t been gene flow between closely related species. the reality is that the ‘biological species concept’ is probably not valid across most taxa because of non-trivial gene flow. but people draw lines anyway.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    also, the rate of change is not constant. due to the nature of geography and population density you do see a greater rate of change across the sahara. the mozabite – taureg – fulani continuum for example exhibits much greater jumps in Fst per unit than a similar one on the north european plain. additionally, if you weight by population you see that the ‘connecting’ group, the taureg, are very sparse. this obviously matters for them being mediators of gene flow. the fact that west sahel populations have the eurasian LP allele and th east sahel ones have their own unique ones illustrates this.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    vineviz, also, by your criterion of explicit encapsulated boundedness of nature or representation it seems that terms such as mountains, hills, rivers, streams, gravity wells, planets, moons, life, etc. can all be problematized. i agree that a specific elevation and grade is scientifically much preferable to distinguishing between ‘mountains’ and ‘hills,’ but in conventional verbal discussion it starts to get ridiculous.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    also add gene to the list.

  • vineviz

    . yes, stupid people may look at a tree and forget abut intra-pop variance or the reticulation which is elided, but non-stupid people have already discounted that.

    Perhaps, but I think it is no accident that the “non-stupid” people generally are not using the word “race” in anything like the traditional sense.

    By the way I agree with you about the non-constancy of clinal gradation, though I do think true discontinuities are clearly the exception not the norm.

    I also agree that “race as a social construct” is not a unique problem (though the social baggage it carries does probably put it in a different class than, say discussions about whether Pluto is a planet or not). Color (electromagentic radiation) is another good analogy, by the way: most people clearly think of red as distinct from orange or yellow. But there not a non-arbitary point in the spectrum where this transition obviously happens from a purely physical perspective. Color is a social construct too, in that way.

  • Chris T

    Vincent: You have heard of probability distributions, right? A single loci has a higher probability of being found in one population than another. Now, one loci can’t tell you much on its own, but get enough of them and certain loci will correlate together more than others.

    Look along the continuum and you’ll find a number of distinct peeks in the distribution of loci correlates where the majority of people from a particular group fall. We can identify and name those peaks (as Razib has said numerous times, you can call them whatever you want). Is the probability that a person will be correctly assigned 100 percent? No, of course not, and no one here is claiming that.

    This matters because, despite remarks to the contrary above, the typical racial classification schema do imply a clean phylogenetic relationship in which intraracial relationships are stronger than interracial relationships. But the science simply doesn’t bear this out.

    No one on this thread has said you could create clean relationships. What has been said is that people can be assigned to a particular population groups from particular geographic locations with a high degree of confidence based on their genetics.

    BTW, I work in medical research and we most certainly do treat population groups (‘races’) as identifiable and significant.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Perhaps, but I think it is no accident that the “non-stupid” people generally are not using the word “race” in anything like the traditional sense.

    look, the problem is that lay people (including intelligent) are boxed into two positions:

    1) platonic races

    2) a genetically flat world where discussion of variation is rendered moot because of a presumed lack of pattern or structure

    the reality is that there are positions in the interval. what i try to do is flesh out that position. you may think #2 is ludicrous, but i know that most well educated people do not. in large part because of the rhetoric of race-is-an-illusion. stuff like this:

    http://raceandgenomics.ssrc.org/

    actually ends up confusing people in my opinion. if you read the anti-race authors they throw around a lot of terms, but a lot of the time it’s hard to figure out what they’re trying to say that’s not #2, though they clearly are.


    By the way I agree with you about the non-constancy of clinal gradation, though I do think true discontinuities are clearly the exception not the norm.

    yes. and interestingly those exceptions tend to shake out around the lines of the ‘classical races’.

    http://en.wikipedia.org/wiki/File:Meyers_b11_s0476a.jpg

  • vineviz

    No one on this thread has said you could create clean relationships.

    Actually, at least one person has said that. But you’re not saying that, so we probably agree on this point.

    What has been said is that people can be assigned to a particular population groups from particular geographic locations with a high degree of confidence based on their genetics.

    I think you probably overestimate that “degree of confidence”, in part because most studies on this topic which you might cite to back up your statement have – in fact – used such sparse sampling that the “clean” assignation is more an artifact of the methodology than a reflection of reality.

    razib has a valid point in his prior comment, which is that the general population probably has much more radical views on race than the readers of his blog do. As you say, no one is arguing for the “platonic” view of race nor is anyone taking the “no signifcant variation” position either.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    which is that the general population probably has much more radical views on race than the readers of his blog do.

    i think it would be accurate to say that compared to my readership the general population are unsubtle (they’re either stupid or ignorant, or both). a substantial number of my readers are pretty shocking hereditarians i’d say compared to the general population, while some of them are racial nationalists of some sort (you don’t see those comments because obviously i’m not going to publish that sort of thing). IOW, i think the dispersion of normative views is greater than in the general population, though there’s probably a rough consensus on matters of positive fact.

  • Insightful

    BTW, I work in medical research and we most certainly do treat population groups (’races’) as identifiable and significant

    Yeah, but I bet you wouldn’t start prescribing ‘race-based’ medicine based on racial classifications. The reason why is because it goes back to what Vincent had said. Things are not cut and dry. We are all on a continuum whether you or I like it or not… And what about Fijians, Andaman islanders, native Tasmanians, Solomon islanders, New Guineans? If you were treating these people like people of African descent because they were visibly similar at glance you would be seriously mistaken. They are among the furthest peoples away from Africans genetically speaking…

  • http://www.iSteve.blogspot.com Steve Sailer

    The central confusion in this discussion that could be easily resolved is that racial groups are less genetic than genealogical. Racial groups are not defined by genes but by genealogy. We can use genes to get some sense of missing genealogical information, but the genes don’t define race, no more than skin color does.

    Imagine some simple genetic mutation that is 100% fatal before the child reaches the age of reproduction. Are all the victims of this mutation a race? No, because race implies (according to definition #1 in my dictionary) lineage.

    Similarly, consider the quite black skinned professional golfer Vijay Singh, who was the only man in the last decade to displace Tiger Woods from the #1 position. He’s much darker in coloration than Woods, but I’ve searched Google and no American sportswriter has ever called Singh black or African-American. His genealogy comes from South Asia, not from Africa in recent millennia, so, rightly, nobody ever thinks of him as African.

    All the criticisms that can be made about the concept of racial groups can be made about the concept of extended families.

    For example, last week a friend told me about how on Sunday after Mass, he had introduced his nieces to Gov. Schwarzenegger’s teenage sons, and then the young people started flirting up a storm. I joked that his future great-nephews and great-nieces would be Schwarzeneggers. But then, I realized, if so, they would also be Shrivers — a famous liberal Catholic clan (Sargent Shriver was the Democratic VP candidate in 1972). And then, when I stopped to think about it, they would also be Kennedys.

    The conundrums of extended family membership — How can you belong to more than one extended family? How do you decide where one extended family ends? — are even more fuzzy than racial group membership, yet nobody argues that extended families don’t exist.

    In fact, racial groups are simply more coherent subsets of extended families, made more identifiable by some degree of inbreeding. Every human is related genealogically to every other human, but everybody is more related genealogically to some people than to other people.

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    Yeah, but I bet you wouldn’t start prescribing ‘race-based’ medicine based on racial classifications. The reason why is because it goes back to what Vincent had said. Things are not cut and dry. We are all on a continuum whether you or I like it or not…

    well, a lot of the study groups are constrained to a particular population, right? the biggest thing about ‘race based medicine’ as a brown dude is to be really careful of extrapolating too much from samples of northern europeans. granted, if the effect size is big i generally assume it’s all good. though there’s so many false positives in medicine as a whole it’s kind of moot….

  • http://www.iSteve.blogspot.com Steve Sailer

    Conversely, it’s worth noting the amount of genetic variation within even nuclear families. Consider siblings who are successful in the same business. If you ask a casting director, they would say that Jeff Bridges competes more for parts with Dennis Quaid than with Beau Bridges, and that Randy Quaid (when sane) competes more with Beau than with his own brother Dennis.

    Yet, it would be inane to say, “Families don’t exist!” or that “Siblingship is just a social construction!”

  • Chris T

    Yeah, but I bet you wouldn’t start prescribing ‘race-based’ medicine based on racial classifications.

    Treatments? No. Diagnostics and prevention? Yes.

    ie: Genetic testing for individuals is expensive at this time and, even though a large number of tests for different genetic diseases exist, the full range is rarely, if ever, tested for. Certain genetic diseases are far more likely to appear in some populations than others (ie: Tay Sachs in Ashkenazi Jews and Sickle Cell in Africans). When deciding what to test for, the racial identification of the person is taken into account.

  • dan

    http://projects.nytimes.com/census/2010/explorer?ref=us

    then i guess the NYT outed themselves as having “radical” views on race today

  • http://dienekes.blogspot.com Dienekes

    If you sample just two distant populations (say, one small village in southern Italy and another in northern Finland) you may indeed be able to concoct a PCA or cluster analysis that will result in 100% of the Italians in one group and 100% of the Finns in the other. As razib might say, it’s “not that hard”

    You vastly underestimate the ability to classify people correctly at very short geographical distances. You don’t have to go to southern Italy to find people that can be distinguished from Finns 100% of the time, you can tell Finns from their immediate neighbors 100% of the time.

    http://dodecad.blogspot.com/2010/12/genetic-structure-in-north-central.html

    You can classify neighboring Armenians/Assyrians 93% of the time

    http://dodecad.blogspot.com/2010/12/assyrians-vs-armenians.html

    You can distinguish Ashkenazi from Sephardic Jews with 95% success

    http://dienekes.blogspot.com/2010/11/cluster-galore-re-analysis-of-behar-et.html

    You can distinguish French from French Basque with 100% success

    http://dienekes.blogspot.com/2010/11/clusters-galore-in-hgdp-panel.html

    The claim that the ability to cluster individuals is due to ‘sparse sampling’ is further invalidated by the fact that it can be done with 139 different populations. Filling in the gaps of geographical sampling does not make largely disjoint clusters disappear

    http://dienekes.blogspot.com/2010/12/human-genetic-variation-124-clusters.html

  • http://www.kinshipstudies.org German Dziebel

    “@ German Dziebel : With one locus, cluster boundaries are fuzzy, with multiply loci they are more solid and keep recurring no matter what loci you throw into the mix.

    Sorry, but that’s not true at all.

    What appear to be “solid” boundaries in the PCA plots you are used to observing in papers is simply an artifact of sparse sampling…”

    You’re slipping into talking about geography, not genetics. What your example demonstrates at the most is that any “race” can be subdivided into subclusters, or that a metacluster has been overlooked, or that a cluster is in fact a subcluster of a more inclusive cluster or that there are some emerging clusters. since emerging clusters are small, their boundaries are indeed fuzzy. if you want to seriously undermine cluster thinking you should demonstrate that those clusters are based on homoplasies and share no identity by descent.

  • biologist

    @ German Dziebel #60 —

    “What appear to be “solid” boundaries in the PCA plots you are used to observing in papers is simply an artifact of sparse sampling…””

    how do you interpret the “village” figure?

    [that’s vineviz actually, german is quoting him -R]

  • biologist

    R — Thanks for fixing that.

    vineviz — Sparse sampling was a plausible hypothesis circa 2004 (http://www.ncbi.nlm.nih.gov/pubmed/15342553) but even by 2005 it had already been addressed (http://www.ncbi.nlm.nih.gov/pubmed/16355252) and seems to be refuted by the available data today.

    This post in particular is amazing:
    http://dienekes.blogspot.com/2010/12/human-genetic-variation-124-clusters.html

  • http://blogs.discovermagazine.com/gnxp Razib Khan

    there seem to be two separate issues, which luke jostins clarified in twitter regarding my post, which i confounded unfortunately

    1) variation

    2) structure

    the main issue in terms of lewonton et al. is that as cavalli-sforza implied it seems that they want to reject #2 so as to obviate awkwardness with #1. but even if you reject #2, that doesn’t necessarily mean that #1 is not going to be an issue. i think we kind of acknowledge #1 here already, and are haggling over the nature of #2. that’s fine. but from a perspective of politically/socially explosive findings, #1 is where it’s at, #2 or not (this is how cavalli-sforza managed to get his work in the 1990s widely accepted, focusing on neutral markers and ignoring by and large functional variants which are a subset of #1).

  • Hamranhansenhansen

    Yeah, racism is not that hard. We already knew that.

  • jld

    @Hamranhansenhansen

    Yeah!
    Very annoying to the moonbats just like evolution is annoying to most wingnuts.
    What a pity that science is so vexing to political whackos.

  • http://washparkprophet.blogspot.com ohwilleke

    “You can classify neighboring Armenians/Assyrians 93% of the time

    You can distinguish Ashkenazi from Sephardic Jews with 95% success

    You can distinguish French from French Basque with 100% success”

    But try to distinguish the Bronx from the Upper West Side and you’ve got real problems.

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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

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